In the presence of non-genotyped founders, allele frequency estimates are of paramount importance for IBD estimation. The large differences in allele frequencies between Whites and African Americans for microsatellites have been well established. Our group identified similar differences for allele frequencies of SNPs [5]. Because of this all of our analyses were restricted to 112 of the 143 pedigrees in which the entire pedigree was unambiguously White (as determined by self report and STRUCTURE) [5]. These pedigrees had an average of 9.3 individuals typed per pedigree (range: 5–27). Maximum likelihood estimators (MLE) for allele frequencies for both SNPs and microsatellites were computed using the 'freq mle' option in SOLAR [6].
